How to install GROMACS

If you’re delving into the captivating realm of molecular modeling, chances are you’ve come across GROMACS a popular tool for molecular simulations.

As a beginner, it may seem intimidating to go through the installation procedure for this software.

In this article, I will show you how to quickly install GROMACS on your machine. Take it easy, in most cases it’s a quick and straightforward endeavor that will take just a few minutes.

How to install GROMACS on Linux

MD simulations require significant computational resources, making common laptop or desktop hardware unsuitable for running them effectively.

To perform most MD simulations, high-performance computing clusters or specially designed GPU workstations are typically required. Although GROMACS has the capability to run on a laptop, it is generally recommended not to rely on such setups.

Linux is the preferred platform for MD simulations. Therefore, we’ll start by looking at the process to install GROMACS on a Linux machine. Below are the six simple steps to get you started:

1. Update Your Packages

Ensure your system is up to date by running these commands:

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sudo apt update 
sudo apt upgrade

2. Install Prerequisites

Before diving into GROMACS installation, ensure you have these two essential prerequisites installed: cmake and build-essential.

Let’s start by installing cmake.

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sudo apt install cmake

You can check the version with:

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cmake -version

Now we can proceed to install build-essential:

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sudo apt install build-essential

3. Download and Unpack your Desired GROMACS Version

Now, let’s assume you are interested in GROMACS 2022.3.

To get started, the first thing you should do is download the tarball of this specific version of GROMACS. You can access a list of all available GROMACS versions here. Once you’ve made your selection, proceed to download and unpack the GROMACS version you need, in this example, GROMACS 2022.3.

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wget https://ftp.gromacs.org/gromacs/gromacs-2022.3.tar.gz
tar xvf gromacs-2022.3.tar.gz

4. Create a Build Directory

Now create a build directory and move into it.

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cd gromacs-2022.3
mkdir build
cd build

5. Compile and Install GROMACS

Now, it’s time to compile the source code and install GROMACS:

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cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSION_DOWNLOAD=ON
make 
make check 
sudo make install

To check the version you can still use the gmx -version command.

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cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSION_DOWNLOAD=ON -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/path/to/dir
make 
make check 
sudo make install

6. Activate GROMACS

Activate GROMACS by using the following command every time you open a new terminal session:

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source /usr/local/gromacs/bin/GMXRC

Please note that if you opted to install it in a different directory, make sure to source from that specific location.

Once you are done with the installation you may be interested in proceeding with a hands-on GROMACS tutorial.

How to install GROMACS on MacOS

In this section, I’ll guide you through two straightforward methods for getting GROMACS up and running on your Mac. You have two options:

1. The Homebrew Approach: Using the Homebrew package manager
2. The Recommended Method: The standard procedure for building GROMACS

Now, let’s dive into each of these methods, so you can choose the one that suits you best.

Quick and Easy: Install GROMACS with Homebrew

The first approach to installing GROMACS is the “quick and dirty” method. If you prefer a more customizable installation, I’ll walk you through the recommended approach in the next section. But for now, let’s dive into this straightforward option.

1. Installing Homebrew

If you don’t already have homebrew installed just follow the instructions on this link. Don’t worry, you will just need to copy and paste a couple of commands into your terminal. The whole process should take no more than a few minutes.

2. Installing GROMACS with the brew command

Once Homebrew is up and running on your system, we’re ready to proceed with the GROMACS installation. Open your terminal and use the brew command as shown below:

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brew install gromacs

Congratulations. You have just installed GROMACS on your Mac.

3. Verify the installation was correct

Congratulations. You have just installed GROMACS on your Mac. To verify that everything proceeded according to our plans you can type the following command:

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gmx -version

This command should display the GROMACS version as well as other information on the software.

Install with the standard procedure

If you’re looking for a specific version of GROMACS or desire more control over your installation, the standard approach outlined in the official guide is your best bet. Keep in mind that this method offers greater customization but will take a bit more time compared to the previous method.

1. Preparing Dependencies

Before diving into GROMACS installation, ensure you have a couple of essential tools in place. If you don’t already have them, use Homebrew to install wget and cmake with these commands:

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brew install cmake 
brew install wget

2. Download and Compile GROMACS

From here on the procedure is very similar to the one reported above for Linux.

Let’s say that you are interested in GROMACS 2020.5. The first thing you should do is download the tarball of this specific version of GROMACS. You can find all the available GROMACS versions here.

Go to the folder where you want to download the program (e.g., Applications) and install GROMACS via wget.

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wget https://ftp.gromacs.org/gromacs/gromacs-2020.5.tar.gz

When the download is over you can unpack the file with tar:

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tar xvf gromacs-2020.5.tar.gz

Change directory:

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cd gromacs-2020.5

Make a new directory named build and move inside it.

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mkdir build
cd build

Type this command:

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cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSION_DOWNLOAD=ON

Now you need to run a sequence of three commands to compile the source code. This will get some time to complete.

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make 
make check 
sudo make install

Now you have successfully installed GROMACS on your machine. To activate it you have to source it with the following command.

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source /usr/local/gromacs/bin/GMXRC

To check the version you can still use the gmx -version command we previously saw.